I have been a webmaster for around 12 years, but only a coder for 2.5 years. I have been a single man team coding projects for myself. However, I am noticing a market for the type of apps I create and I do not know where to begin with what I need to do to implement a system to sell my scripts on a monthly fee basis or a per domain basis. I have been creating web apps with codeigniter and although I don't mind a client seeing the framework, I would prefer hiding these files or encoding them so I present myself a little more professional.
Since I am a single man team, I never had to worry much about version control, encoding my code, and licensing.
I would greatly appreciate someone taking the time to put me on the correct path of how to accomplish a solid system for controlling and selling my web applications.
You should look into ZendGuard or Cube. Those applications will "crypt" your code and have the feature to make a license file that will prevent the application from functionning if not valid or not available. Using this you can make it more safe.
Now for the monthly fee business it depends on how you expect to make your application available to your customers. If they need to download the source code and install it on a server, you have no choice but to generate a license file each end of the month (though this can be scripted) and send it to the customer so he can update it on his server. If your application is in fact a service that is remotly call from the customer server you need to add infos on the customer identity in the remote call so you can check on your side if he has the right to execute what he is asking for.